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- PDB-4yua: Glycogen phosphorylase in complex with ellagic acid -

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Basic information

Entry
Database: PDB / ID: 4yua
TitleGlycogen phosphorylase in complex with ellagic acid
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Chem-REF / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKyriakis, E. / Kantsadi, L.A. / Stravodimos, A.G. / Chatzileontiadou, S.M.D. / Leonidas, D.D.
CitationJournal: Febs Lett. / Year: 2015
Title: Natural flavonoids as antidiabetic agents. The binding of gallic and ellagic acids to glycogen phosphorylase b.
Authors: Kyriakis, E. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S. / Skamnaki, V.T. / Leonidas, D.D.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9723
Polymers97,4221
Non-polymers5492
Water4,972276
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9436
Polymers194,8452
Non-polymers1,0994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5880 Å2
ΔGint-18 kcal/mol
Surface area56950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.480, 128.480, 116.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1276-

HOH

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Components

#1: Protein Glycogen phosphorylase, muscle form / / Myophosphorylase


Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-REF / 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione / Ellagic acid, 4,4',5,5',6,6'-Hexahydroxydiphenic acid 2,6,2',6'-dilactone / Ellagic acid


Mass: 302.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES buffer

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→38.35 Å / Num. obs: 63707 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rsym value: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→38.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.83 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20178 3111 4.9 %RANDOM
Rwork0.17289 ---
obs0.17428 60595 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 37 276 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9589213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92823.553349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.347151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8481559
X-RAY DIFFRACTIONr_chiral_restr0.0910.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215229
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.422.7693243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3274.1434050
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1283.1273554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.53124.40210447
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 258 -
Rwork0.251 4478 -
obs--98.56 %

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